12-49891779-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000320634.8(FAIM2):​c.435-665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,086 control chromosomes in the GnomAD database, including 7,054 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.28 ( 7054 hom., cov: 32)

Consequence

FAIM2
ENST00000320634.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.768
Variant links:
Genes affected
FAIM2 (HGNC:17067): (Fas apoptotic inhibitory molecule 2) Involved in regulation of neuron apoptotic process. Acts upstream of or within negative regulation of extrinsic apoptotic signaling pathway via death domain receptors. Located in membrane raft. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FAIM2NM_012306.4 linkuse as main transcriptc.435-665G>A intron_variant ENST00000320634.8 NP_036438.2
FAIM2XM_005268730.4 linkuse as main transcriptc.309-665G>A intron_variant XP_005268787.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FAIM2ENST00000320634.8 linkuse as main transcriptc.435-665G>A intron_variant 1 NM_012306.4 ENSP00000321951 P1Q9BWQ8-1

Frequencies

GnomAD3 genomes
AF:
0.279
AC:
42337
AN:
151968
Hom.:
7052
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.101
Gnomad AMI
AF:
0.429
Gnomad AMR
AF:
0.252
Gnomad ASJ
AF:
0.463
Gnomad EAS
AF:
0.224
Gnomad SAS
AF:
0.325
Gnomad FIN
AF:
0.365
Gnomad MID
AF:
0.323
Gnomad NFE
AF:
0.368
Gnomad OTH
AF:
0.295
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.278
AC:
42335
AN:
152086
Hom.:
7054
Cov.:
32
AF XY:
0.279
AC XY:
20742
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.101
Gnomad4 AMR
AF:
0.252
Gnomad4 ASJ
AF:
0.463
Gnomad4 EAS
AF:
0.224
Gnomad4 SAS
AF:
0.325
Gnomad4 FIN
AF:
0.365
Gnomad4 NFE
AF:
0.368
Gnomad4 OTH
AF:
0.291
Alfa
AF:
0.345
Hom.:
6640
Bravo
AF:
0.258
Asia WGS
AF:
0.231
AC:
806
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
3.4
DANN
Benign
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17201502; hg19: chr12-50285562; API